+Open data
-Basic information
Entry | Database: PDB / ID: 8ho6 | |||||||||
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Title | ScRIPK WT | |||||||||
Components | ScRIPK kinase protein | |||||||||
Keywords | PLANT PROTEIN / Kinase / RLCK VII | |||||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE Function and homology information | |||||||||
Biological species | Saccharum hybrid cultivar (sugarcane) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Fang, J.L. / Zhang, M.Q. | |||||||||
Funding support | 2items
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Citation | Journal: Front Plant Sci / Year: 2023 Title: Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis. Authors: Fang, J. / Chai, Z. / Huang, R. / Huang, C. / Ming, Z. / Chen, B. / Yao, W. / Zhang, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ho6.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ho6.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ho6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ho6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ho6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ho6_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 8ho6_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8ho6 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8ho6 | HTTPS FTP |
-Related structure data
Related structure data | 8hoaC 8hodC 5tosS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36416.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharum hybrid cultivar (sugarcane) / Gene: NCGR_LOCUS634 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 40% v/v Polyethylene glycol 400, 0.19 mM Cymal-7, 10% v/v Polyethylene glycol 3350, 0.18 mM GDN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2021 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→32.06 Å / Num. obs: 23842 / % possible obs: 99.7 % / Redundancy: 12.79 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Χ2: 1.02 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.15 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 23842 / CC1/2: 0.853 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TOS Resolution: 2.1→26.738 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→26.738 Å
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Refine LS restraints |
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LS refinement shell |
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